在 R 中，當使用 tip.color() 為 phylog.netic 樹着色時，如何選擇 colors 並添加圖例？

Question

我有一棵看起來像這樣的樹；

# Create tree
library(phytools)
sim.tree<-pbtree(n=18)
plot(sim.tree)

我有一個帶有我的特征的數據框（一個 class 因子的向量）像這樣着色；

# data frame with vector to color tree with
df<-data.frame(tip = paste0("t", 1:18),
               vector.to.color.with = as.factor(c("<10", "10-20", "10-20", "10-20", "NA", "10-20", 
                                   "10-20", "10-20", "20-35", "<10", "10-20", "<10", 
                                   "35", "20-35", "<10", "NA", "10-20", "<10")))

在 SO 的大力幫助下，我能夠像這樣給提示標簽上色；

cols <- as.integer(df$vector.to.color.with[match(sim.tree$tip.label,df$tip)])
plot(sim.tree, tip.color = cols)

我現在想選擇自己的colors，加上圖例。 任何幫助是極大的贊賞。

Answer 1

這是一個帶有自定義 colors 的版本：

library(dplyr)
library(phytools)
## library(RColorBrewer)

# Create tree
df<-data.frame(tip = paste0("t", 1:18),
               brk = as.factor(c("<10", "10-20", "10-20", "10-20", "NA", "10-20", 
                                 "10-20", "10-20", "20-35", "<10", "10-20", "<10", 
                                 "35", "20-35", "<10", "NA", "10-20", "<10"))) |>
  mutate(color = recode(brk,
                        "<10"   = "red",
                        "10-20" = "green",
                        "NA"    = "gray",
                        "20-35" = "blue",
                        "35"    = "black"))
  ## mutate(color = brewer.pal(6, "Set1")[brk])


set.seed(123)
sim.tree<-pbtree(n=18)
cols <- with(df, as.character(color[match(sim.tree$tip.label, tip)]))


plot(sim.tree, tip.color = cols, x.lim = c(0,3))


with(df,
     legend(x=2.5, y=10,
            legend = levels(brk),
            ## col = brewer.pal(6, "Set1"),
            col = as.character(levels(color)),
            pch = 20,
            box.lwd = 1))

這里有一個RColorBrewer的解決方案，它提供了已經很漂亮的調色板。

library(dplyr)
library(phytools)
library(RColorBrewer)

# Create tree
df<-data.frame(tip = paste0("t", 1:18),
               brk = as.factor(c("<10", "10-20", "10-20", "10-20", "NA", "10-20", 
                                 "10-20", "10-20", "20-35", "<10", "10-20", "<10", 
                                 "35", "20-35", "<10", "NA", "10-20", "<10"))) |>
  ## mutate(color = recode(brk,
  ##                       "<10"   = "red",
  ##                       "10-20" = "green",
  ##                       "NA"    = "gray",
  ##                       "20-35" = "blue",
  ##                       "35"    = "black"))
  mutate(color = brewer.pal(6, "Set1")[brk])


set.seed(123)
sim.tree<-pbtree(n=18)
cols <- with(df, color[match(sim.tree$tip.label, tip)])


plot(sim.tree, tip.color = cols, x.lim = c(0,3))


with(df,
     legend(x=2.5, y=10,
            legend = levels(brk),
            col = brewer.pal(6, "Set1"),
            ## col = as.character(levels(color)),
            pch = 20,
            box.lwd = 1))